Publication details

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

Investor logo


Year of publication 2013
Type Article in Periodical
Magazine / Source Journal of Chemical Theory and Computation
MU Faculty or unit

Central European Institute of Technology

Field Physical chemistry and theoretical chemistry
Keywords phosphorus chemical shift nucleic acids MD DFT
Description This work addresses the question of the ability of the MD/DFT approach to reproduce sequence trend in 31P chemical shifts (delta_P) in the backbone of nucleic acids. delta_P for [d(CGCGAATTCGCG)]2 have been computed using DFT calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of 31P chemical shifts for two distinct B-DNA subfamilies BI and BII, delta_P/BI and delta_P/BII, have been determined as averages over the BI and BII subparts of the MD trajectory. This has been done for various samplings of MD trajectory and for two sizes of both the model and the solvent embedding. For all of the combinations of trajectory sampling, model size, and embedding size, sequence dependence of delta_P/BI in the order of 0.4–0.5 ppm has been obtained. Weighted averages for individual 31P nuclei in the studied DNA double-helix have been calculated from delta_P/BI and delta_P/BII using BI and BII percentages from free MD simulations as well as from approaches employing NMR structural restraints. A good qualitative agreement is found between experimental sequence trends in delta_P and theoretical delta_P employing short (24 ns) MD run and BI, BII percentages determined by Hartmann et al. or via MD with the inclusion of NMR structural restraints. Theoretical delta_P exhibit a systematic offset of ca. 11 ppm and overestimation of trends by a factor of ca. 1.7. When scaled accordingly, theoretical delta_P/BI and delta_P/BII can be used to determine the expected percentage of BII to match the experimental value of delta_P. The systematic offsets of the theoretical delta_P obtained by MD/DFT approach result primarily from the unrealistic bond lengths employed by classical MD. The findings made in this work provide structure-delta_P relationships for possible use as NMR restraints and suggest that NMR calculations on MD snapshots can be in the future employed for the validation of newly developed force fields.
Related projects:

You are running an old browser version. We recommend updating your browser to its latest version.

More info